Antigen persists in discrete cell subsets within the lymph node
Ag-score is shown for all LEC subsets for each experiment
Ag-score is shown for all DC subsets for each experiment
Day 21 Ag-score is shown for all subsets for each experiment
Day 42 Ag-score is shown for all subsets for each experiment
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
## [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
##
## time zone: America/Denver
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 tools grid stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] ggtree_3.8.2 GOSemSim_2.26.1 org.Mm.eg.db_3.17.0
## [4] AnnotationDbi_1.62.2 IRanges_2.34.1 S4Vectors_0.38.2
## [7] Biobase_2.60.0 BiocGenerics_0.46.0 msigdbr_7.5.1
## [10] enrichplot_1.20.3 clusterProfiler_4.8.3 caret_6.0-94
## [13] lattice_0.21-8 furrr_0.3.1 future_1.33.0
## [16] ranger_0.15.1 rsample_1.2.0 harmony_1.1.0
## [19] biomaRt_2.56.1 openxlsx_4.2.5.2 MetBrewer_0.2.0
## [22] ggtext_0.1.2 ggtrace_0.2.0 qs_0.25.5
## [25] vroom_1.6.4 M3Drop_1.26.0 numDeriv_2016.8-1.1
## [28] djvdj_0.1.0 gtools_3.9.4 clustifyrdata_1.1.0
## [31] here_1.0.1 presto_1.0.0 data.table_1.14.8
## [34] Rcpp_1.0.11 devtools_2.4.5 usethis_2.2.2
## [37] ComplexHeatmap_2.16.0 patchwork_1.1.3 scales_1.2.1
## [40] boot_1.3-28.1 clustifyr_1.12.0 mixtools_2.0.0
## [43] broom_1.0.5 colorblindr_0.1.0 colorspace_2.1-0
## [46] xlsx_0.6.5 RColorBrewer_1.1-3 ggrepel_0.9.3
## [49] cowplot_1.1.1 knitr_1.44 gprofiler2_0.2.2
## [52] SeuratObject_4.1.4 Seurat_4.4.0 ggforce_0.4.1
## [55] ggbeeswarm_0.7.2 lubridate_1.9.3 forcats_1.0.0
## [58] stringr_1.5.0 dplyr_1.1.3 purrr_1.0.2
## [61] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
## [64] ggplot2_3.4.3 tidyverse_2.0.0
##
## loaded via a namespace (and not attached):
## [1] igraph_1.5.1 ica_1.0-3
## [3] plotly_4.10.2 Formula_1.2-5
## [5] zlibbioc_1.46.0 tidyselect_1.2.0
## [7] bit_4.0.5 doParallel_1.0.17
## [9] clue_0.3-65 rjson_0.2.21
## [11] blob_1.2.4 urlchecker_1.0.1
## [13] S4Arrays_1.0.6 parallel_4.3.1
## [15] png_0.1-8 cli_3.6.1
## [17] ggplotify_0.1.2 goftest_1.2-3
## [19] kernlab_0.9-32 densEstBayes_1.0-2.2
## [21] uwot_0.1.16 shadowtext_0.1.2
## [23] curl_5.1.0 mime_0.12
## [25] evaluate_0.22 tidytree_0.4.5
## [27] leiden_0.4.3 stringi_1.7.12
## [29] pROC_1.18.5 backports_1.4.1
## [31] XML_3.99-0.14 httpuv_1.6.11
## [33] magrittr_2.0.3 rappdirs_0.3.3
## [35] splines_4.3.1 prodlim_2023.08.28
## [37] RApiSerialize_0.1.2 ggraph_2.1.0
## [39] sctransform_0.4.0 sessioninfo_1.2.2
## [41] DBI_1.1.3 jquerylib_0.1.4
## [43] withr_2.5.1 class_7.3-22
## [45] rprojroot_2.0.3 lmtest_0.9-40
## [47] bdsmatrix_1.3-6 tidygraph_1.2.3
## [49] htmlwidgets_1.6.2 fs_1.6.3
## [51] SingleCellExperiment_1.22.0 segmented_1.6-4
## [53] labeling_0.4.3 MatrixGenerics_1.12.3
## [55] reticulate_1.32.0 zoo_1.8-12
## [57] XVector_0.40.0 timechange_0.2.0
## [59] foreach_1.5.2 fansi_1.0.5
## [61] caTools_1.18.2 timeDate_4022.108
## [63] irlba_2.3.5.1 gridGraphics_0.5-1
## [65] ellipsis_0.3.2 lazyeval_0.2.2
## [67] yaml_2.3.7 survival_3.5-5
## [69] scattermore_1.2 crayon_1.5.2
## [71] RcppAnnoy_0.0.21 progressr_0.14.0
## [73] tweenr_2.0.2 later_1.3.1
## [75] ggridges_0.5.4 codetools_0.2-19
## [77] base64enc_0.1-3 GlobalOptions_0.1.2
## [79] profvis_0.3.8 KEGGREST_1.40.1
## [81] bbmle_1.0.25 Rtsne_0.16
## [83] shape_1.4.6 filelock_1.0.2
## [85] foreign_0.8-84 pkgconfig_2.0.3
## [87] xml2_1.3.5 GenomicRanges_1.52.1
## [89] aplot_0.2.2 spatstat.sparse_3.0-2
## [91] ape_5.7-1 viridisLite_0.4.2
## [93] xtable_1.8-4 plyr_1.8.9
## [95] httr_1.4.7 globals_0.16.2
## [97] hardhat_1.3.0 pkgbuild_1.4.2
## [99] beeswarm_0.4.0 htmlTable_2.4.2
## [101] checkmate_2.3.0 nlme_3.1-162
## [103] loo_2.6.0 HDO.db_0.99.1
## [105] dbplyr_2.3.4 digest_0.6.33
## [107] Matrix_1.6-1.1 farver_2.1.1
## [109] tzdb_0.4.0 reshape2_1.4.4
## [111] ModelMetrics_1.2.2.2 yulab.utils_0.1.0
## [113] viridis_0.6.4 rpart_4.1.19
## [115] glue_1.6.2 cachem_1.0.8
## [117] BiocFileCache_2.8.0 polyclip_1.10-6
## [119] Hmisc_5.1-1 generics_0.1.3
## [121] Biostrings_2.68.1 mvtnorm_1.2-3
## [123] parallelly_1.36.0 pkgload_1.3.3
## [125] statmod_1.5.0 pbapply_1.7-2
## [127] SummarizedExperiment_1.30.2 gson_0.1.0
## [129] utf8_1.2.3 gower_1.0.1
## [131] graphlayouts_1.0.2 StanHeaders_2.26.28
## [133] gridExtra_2.3 shiny_1.7.5
## [135] lava_1.7.3 GenomeInfoDbData_1.2.10
## [137] RCurl_1.98-1.12 memoise_2.0.1
## [139] rmarkdown_2.25 downloader_0.4
## [141] RANN_2.6.1 stringfish_0.15.8
## [143] spatstat.data_3.0-1 rstudioapi_0.15.0
## [145] cluster_2.1.4 QuickJSR_1.0.7
## [147] rstantools_2.3.1.1 spatstat.utils_3.0-3
## [149] hms_1.1.3 fitdistrplus_1.1-11
## [151] munsell_0.5.0 rlang_1.1.1
## [153] GenomeInfoDb_1.36.4 ipred_0.9-14
## [155] circlize_0.4.15 mgcv_1.8-42
## [157] xfun_0.40 remotes_2.4.2.1
## [159] recipes_1.0.8 iterators_1.0.14
## [161] matrixStats_1.0.0 reldist_1.7-2
## [163] abind_1.4-5 rstan_2.32.3
## [165] treeio_1.24.3 rJava_1.0-6
## [167] bitops_1.0-7 ps_1.7.5
## [169] promises_1.2.1 inline_0.3.19
## [171] scatterpie_0.2.1 RSQLite_2.3.1
## [173] qvalue_2.32.0 fgsea_1.26.0
## [175] DelayedArray_0.26.7 GO.db_3.17.0
## [177] compiler_4.3.1 prettyunits_1.2.0
## [179] listenv_0.9.0 tensor_1.5
## [181] MASS_7.3-60 progress_1.2.2
## [183] BiocParallel_1.34.2 gridtext_0.1.5
## [185] babelgene_22.9 spatstat.random_3.1-6
## [187] R6_2.5.1 fastmap_1.1.1
## [189] fastmatch_1.1-4 vipor_0.4.5
## [191] ROCR_1.0-11 nnet_7.3-19
## [193] gtable_0.3.4 KernSmooth_2.23-21
## [195] miniUI_0.1.1.1 deldir_1.0-9
## [197] htmltools_0.5.6.1 RcppParallel_5.1.7
## [199] bit64_4.0.5 spatstat.explore_3.2-3
## [201] lifecycle_1.0.3 zip_2.3.0
## [203] processx_3.8.2 callr_3.7.3
## [205] xlsxjars_0.6.1 sass_0.4.7
## [207] vctrs_0.6.3 spatstat.geom_3.2-5
## [209] DOSE_3.26.2 ggfun_0.1.3
## [211] sp_2.1-0 future.apply_1.11.0
## [213] entropy_1.3.1 bslib_0.5.1
## [215] pillar_1.9.0 gplots_3.1.3
## [217] jsonlite_1.8.7 GetoptLong_1.0.5